Download Reaction dynamics simulation of single and double strand breaks in

3A3
Reaction dynamics simulation of single and double strand breaks in DNAs
(Tohoku University)
OKADA, Tomohiko; OIKAWA, Keita; HISHINUMA, Naoki; HANASAKI, Kouta;
KANNO, Manabu; KONO, Hirohiko
1. Introduction
Damage to robust DNA polymers upon exposure to radiation occurs when single or double DNA
strands break. Radiation damage in DNA is induced by direct and indirect effects of radiation. In the
direct mechanism, the sugar-phosphate backbone is ionized upon exposure to high-energy radiation,
which leads to strands breaks. The sources of indirect effects on strand breaks are heat, OH radicals [1],
and low-energy secondary electrons generated by radiation. Experiments on DNA (in dry form) have
proposed a new paradigm: Even electrons possessing a few electron volts of energy induce strand
breaks through formation of dissociative negative ion states [2].
Recently, Mathur et al. investigated in detail the indirect effects on the strand breaks of plasmid
DNAs [3]. They probed femtosecond laser induced damage to aqueous DNA that results from the
strong-field interaction with water wherein electrons and free radicals are generated in situ. These
produce nicks in DNA under physiological conditions. The experimental results indicate that exposure
to intense femtosecond pulses of 1350 and 2200 nm light induces single strand breaks (SSBs) and
double strand breaks (DSBs) in DNA. Single or multiple OH hits on DNA trigger SSBs or DSBs; at
these wavelengths electrons do not directly induce DNA damage. The scenario that they proposed is
that DSBs are induced mostly by the action of two OH radicals; use of OH scavengers establishes that
the probability of a two-hit event reduces much faster than a one-hit event as the scavenger
concentration is increased. They also concluded that thermal
effects induce SSBs but do not induce DSBs.
The detailed mechanisms of strand break however remain
unclear at a molecular level. We have performed reaction
dynamics simulations for short strand DNAs [4] using the
density-functional based tight-binding (DFTB) method [5].
2. Strand breaks of DNAs in vacuum
We first applied the above approach to short single-strand
DNAs. It has been reported for single-strand DNAs [6] that
Fig. 1. Single-strand break sequence in
the cleavage of the sugar-nucleobase bond (base loss) occurs a short single strand DNA analyzed by
followed by that of the sugar-phosphate bond (strand break) MALDI TOF Mass spectrometry [6]
in MALDI experiments (Fig. 1). Our target single strand DNA of four bases is assumed to be
vibrationally excited up to ~1100 K through electronic relaxation after its exposure to radiation and to
be in vacuum (dray form) after evaporation. In the absence of any surroundings such as counter
cations, a single-strand break occurs via sequential steps:
(i) C-N bond breaking between the base and sugar (deoxyribose pentose) of a nucleoside followed
by hydrogen transfer from the sugar and to the base.
(ii) Cleavage of the C-O bond between neighboring sugar and phosphate, followed by hydrogen
transfer from the sugar to the phosphate.
The observed strand break process following a base loss is consistent with the MALDI analysis
shown in Fig.1 [6], which validates the use of the present DFTB approach for DNA strand breaks. The
timescale up to step (ii) was ~a few hundred ps. From the Arrhenius plot obtained by changing the
temperature, we estimated the activation energy for the strand break to be very low as ~ 1.1 eV. The
single strand DNA is unstable in vacuum; the lifetime is about a few seconds at T=100 ℃.
The dynamics of strand breaks are analyzed from the viewpoint of energy and charge transfer. To
that end, we proposed to divide the potential energy into individual atomic ones {VA} [7]. Each atom
A is then assigned to possess an atom resolved energy (ARE), i.e., KA+VA, where KA is the kinetic
energy of atom A. The ARE can be used to quantify the energetic dynamics of reactions. We also
estimated the charge transfer by Mulliken populations to understand the reactions from the viewpoint
of the electronic theory of organic chemistry. According to these analyses, energy and charge were
shared by the pair of the sugar and base during the process (i) and they were shared by the sugar and
phosphate during the process (ii); no energy and charge transfer to the outside of the pair. The strand
break in a single-strand DNA is regarded as a localized event. For double strand DNAs in vacuum,
we found that they are thermally as unstable as in single strand DNAs in vacuum.
3. Strand breaks in water by OH radicals
We have also simulated the strand breaks of DNAs surrounded by water molecules and counter
cations. We found that DNAs in water are thermally stable because the counter cations suppress global
charge and energy transfer in a DNA as long as the surrounding cations are hydrated. DNAs are
however subject to a different mechanism of strand break if cations go out of the hydration pockets to
approach a DNA. The strand breaks induced by heat were SSBs (no double strand breaks took place),
in line with the experimental observation by Mathur et al [3]. We are currently investigating the effects
of OH radicals on DNA strand breaks. When an OH radical abstracts a hydrogen atom from one of
carbon atoms of the pentose ring, one of the P-O bonds in the phosphate breaks. No DSBs took place
by a single hit of an OH radical even if the radical is highly energetic. A DSB needs the action of at
least two OH radicals. We interpret the double strand break to be an accidental event of two
independent single strand breaks by OH radicals on two different strands, which is consistent with the
idea of a two-hit event of OH radicals [3].
[1] Radical and Radical Ion Reactivity in Nucleic Acid Chemistry, ed. M. D. Greenberg (Wiley, New Jersey,
2009)
[2] B. Boudaiffa, P. Cloutier, D. Hunting, M. A. Huels, and L. Sanche, Science 287, 1658 (2000); X. Pan,
P. Cloutier, D. Hunting, and L. Sanche, Phys. Rev. Lett. 90, 208102 (2003), and references therein.
[3] A. K. Dharmadhikari , H. Bharambe, J. A. Dharmadhikari, J. S. D'Souza, and D. Mathur, Phys. Rev.
Lett. 112, 138105 (2014).
[4] M. Elstner et al., Phys. Rev. B 58, 7260 (1998).
[5] 4−6 base pairs of adenine and. See M. McCullagh et al., J. Phys. Chem. B 112, 11415 (2008).
[6] L. Zhu, G.R. Parr, M.C. Fitzgerald, C.M. Nelson, L.M. Smith, J. Am. Chem. Soc. 117, 6048 (1995).
[7] This idea originates from the partition of the total electronic energy of a molecule in a laser field into
electron configurational energies. See S. Ohmura et al., J. Chem. Phys. 141, 114105 (2014).